• ALPD could inactivate model strains and environmental microbial communities effectively. • Much less VBNC bacteria were left in ALPD system than chlorinated water samples. • ALPD removed i-DNA and e-DNA several times higher than chlorination. • ALPD could effectively remove chlorine-resistant bacteria. Water-borne pathogenic bacteria are always the top priority to be removed through disinfection process in water treatment due to their threat to human health. It was necessary to develop novel disinfection methods since the conventional chlorine disinfection was inefficient in inactivating chlorine-resistant bacteria, inducing the viable but non-culturable (VBNC) bacteria and forming disinfection by-products (DBPs). In this study, the inactivation of four model strains including Gram-negative (G−), Gram-positive (G+) and environmental samples by atmospheric-pressure air-liquid discharge plasma (ALDP) was assessed systematically. The results showed that ALDP was superior in inactivating all of the samples compared with chlorination. During 10 min ALDP treatment, the G− bacteria were completely inactivated, and the G+ one was inactivated by more than 4.61 logs. The inactivation of bacteria from a campus lake and a wastewater treatment plant effluent exceeded 99.82% and 97.78%, respectively. For G− bacteria, ALDP resulted in a much lower (102∼103 times) levels of VBNC cells than chlorination. ALDP could effectively remove the chlorine-resistant bacteria. More than 96.41% of the intracellular DNA and 99.99% of the extracellular DNA were removed, whereas it was only 56.35% and 12.82% for chlorination. ALDP had a stronger ability to destroy cell structure than chlorination, presumably due to the existence of ROS (·OH, 1O 2 and O 2 −). GC-MS analysis showed that ALDP produced less DBPs than chlorination. These findings provided new insights for the application of discharge plasma in water disinfection, which could be complemental or alternative to the conventional disinfection methods. [Display omitted] [ABSTRACT FROM AUTHOR]